Atomistry » Sodium » PDB 5j2d-5jim » 5jea
Atomistry »
  Sodium »
    PDB 5j2d-5jim »
      5jea »

Sodium in PDB 5jea: Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna

Enzymatic activity of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna

All present enzymatic activity of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna:
3.2.1.17;

Protein crystallography data

The structure of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna, PDB code: 5jea was solved by E.Kowalinski, J.Ebert, E.Stegmann, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.69 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.080, 182.530, 250.550, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.9

Other elements in 5jea:

The structure of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna (pdb code 5jea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna, PDB code: 5jea:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 1 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:58.0
occ:1.00
 OG B:SER159 2.5 64.5 1.0
O B:VAL189 2.7 45.7 1.0
O B:GLY191 2.7 47.4 1.0
N B:SER159 3.0 60.9 1.0
N B:GLY191 3.0 58.2 1.0
CB B:SER159 3.1 46.4 1.0
CA B:GLY191 3.4 47.2 1.0
C B:GLY191 3.4 58.0 1.0
C B:VAL189 3.7 49.0 1.0
CA B:SER159 3.7 45.9 1.0
C B:VAL190 3.8 60.3 1.0
O B:TYR157 3.8 46.1 1.0
C B:ILE158 3.9 45.5 1.0
CG B:ARG225 3.9 48.0 1.0
CA B:ILE158 4.0 45.5 1.0
CB B:ARG225 4.1 48.0 1.0
C B:TYR157 4.1 46.1 1.0
N B:ILE158 4.2 45.8 1.0
CB B:TYR157 4.2 49.1 1.0
CA B:VAL190 4.3 57.4 1.0
N B:VAL190 4.3 45.7 1.0
CD B:ARG225 4.3 49.9 1.0
CB B:VAL189 4.5 45.9 1.0
O B:VAL190 4.5 46.7 1.0
CA B:VAL189 4.6 45.9 1.0
CG1 B:VAL189 4.6 46.3 1.0
C B:SER159 4.8 45.5 1.0
N B:LYS192 4.8 54.4 1.0
O B:SER159 4.8 45.4 1.0
CA B:TYR157 4.8 46.6 1.0
O B:ALA221 4.8 59.1 1.0
O B:ILE158 4.9 45.5 1.0

Sodium binding site 2 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 2 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:64.0
occ:1.00
 O B:ASN20 3.3 53.0 1.0
CD2 B:LEU172 4.4 48.2 1.0
C B:ASN20 4.5 49.6 1.0
CD1 B:ILE216 4.8 48.8 1.0
CA B:GLY220 4.8 55.2 1.0
CB B:ARG223 5.0 61.8 1.0
CB B:ASN20 5.0 61.3 1.0

Sodium binding site 3 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 3 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:84.8
occ:1.00
 OG1 F:THR88 2.4 69.5 1.0
O F:GLN90 2.4 51.0 1.0
O F:SER133 2.5 51.3 1.0
N F:SER133 2.8 59.2 1.0
CD1 F:ILE83 2.9 0.7 1.0
OG1 F:THR92 3.0 69.7 1.0
C F:SER133 3.3 50.0 1.0
N F:THR92 3.4 50.8 1.0
C F:GLN90 3.5 52.7 1.0
CB F:THR88 3.5 75.5 1.0
CA F:SER133 3.6 50.0 1.0
C F:GLY91 3.6 51.3 1.0
CA F:GLY91 3.6 51.7 1.0
C F:LYS132 3.8 54.9 1.0
N F:LYS132 3.8 55.5 1.0
CB F:THR92 3.8 65.9 1.0
CA F:LYS132 3.9 53.5 1.0
O F:TYR130 3.9 55.2 1.0
N F:GLY91 4.0 57.6 1.0
CG1 F:ILE83 4.1 86.0 1.0
CA F:THR92 4.2 50.4 1.0
CG2 F:THR88 4.2 69.0 1.0
C F:PRO131 4.3 60.5 1.0
O F:GLY91 4.4 56.4 1.0
N F:GLY134 4.4 49.7 1.0
CB F:SER133 4.6 50.7 1.0
O F:THR88 4.7 64.8 1.0
CA F:THR88 4.8 70.1 1.0
CA F:GLN90 4.8 52.1 1.0
O F:LYS132 4.8 62.2 1.0
N F:GLN90 4.9 51.7 1.0
CA F:PRO131 4.9 53.4 1.0
C F:THR88 4.9 70.6 1.0
O F:PRO131 4.9 51.0 1.0
CA F:GLY134 4.9 49.7 1.0

Sodium binding site 4 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 4 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na1103

b:67.9
occ:1.00
 CE J:MET606 3.8 0.4 1.0
N J:MET606 3.8 64.8 1.0
CD2 J:PHE495 3.9 69.0 1.0
CG J:MET606 4.1 82.9 1.0
CA J:PRO605 4.3 74.3 1.0
CE2 J:PHE495 4.3 68.3 1.0
CB J:MET606 4.3 63.0 1.0
CB J:PRO605 4.6 61.6 1.0
C J:PRO605 4.6 74.2 1.0
SD J:MET606 4.7 0.3 1.0
CA J:MET606 4.7 62.0 1.0
CD2 J:LEU500 5.0 63.9 1.0

Reference:

E.Kowalinski, A.Kogel, J.Ebert, P.Reichelt, E.Stegmann, B.Habermann, E.Conti. Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex. Mol.Cell V. 63 125 2016.
ISSN: ISSN 1097-2765
PubMed: 27345150
DOI: 10.1016/J.MOLCEL.2016.05.028
Page generated: Mon Oct 7 21:52:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy